Development and application of a toolbox for multivariate pattern analysis of functional magnetic resonance imaging data

The combination of functional magnetic resonance imaging (fMRI) and multivariate pattern analysis (MVPA) is a powerful method for investigating brain function, with multiple MVPA methods being applied to the task including Logistic Regression, Support Vector Machines, Neural Networks, and Gaussian Naive Bayes classifiers. Careful review of application of these methods revealed a common process used in most studies; the majority of variations occurring in the implementation choices in key sections such as feature selection or classification algorithms being employed. Thus, it is possible to develop modularised tools for performing MVPA of fMRI data which can be applied in a variety of ways through selection of appropriate components. Development of such a toolbox for use by the University of Birmingham Cognitive Neuroimaging Laboratory is described. The modular design allows for flexible application and provides a basis for development of novel methods, which is explored through implementation of a novel cross-validation method and development of a method for investigating the effects of learning on tuning of neural populations. The development process has resulted in an efficient, robust and reliable toolbox, capable of performing a pre-implemented set of standard multi-variate pattern analyses and provides a basis for further development of novel methods

Decoding the future from past experience: learning shapes predictions in early visual cortex.

Learning the structure of the environment is critical for interpreting the current scene and predicting upcoming events. However, the brain mechanisms that support our ability to translate knowledge about scene statistics to sensory predictions remain largely unknown. Here we provide evidence that learning of temporal regularities shapes representations in early visual cortex that relate to our ability to predict sensory events. We tested the participants' ability to predict the orientation of a test stimulus after exposure to sequences of leftward- or rightward-oriented gratings. Using fMRI decoding, we identified brain patterns related to the observers' visual predictions rather than stimulus-driven activity. Decoding of predicted orientations following structured sequences was enhanced after training, while decoding of cued orientations following exposure to random sequences did not change. These predictive representations appear to be driven by the same large-scale neural populations that encode actual stimulus orientation and to be specific to the learned sequence structure. Thus our findings provide evidence that learning temporal structures supports our ability to predict future events by reactivating selective sensory representations as early as in primary visual cortex.This work was supported by a Wellcome Trust Senior Research Fellowship to AEW (095183/Z/10/Z) and grants to ZK from the Biotechnology and Biological Sciences Research Council [H012508], a Leverhulme Trust Research Fellowship (RF-2011-378) and the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme FP7/2007-2013/ under REA grant agreement no. PITN-GA-2011-290011.This is the published version. It first appeared at http://jn.physiology.org/content/early/2015/02/27/jn.00753.2014

Learning alters the tuning of functional magnetic resonance imaging patterns for visual forms

Learning is thought to facilitate the recognition of objects by optimizing the tuning of visual neurons to behaviorally relevant features. However, the learning mechanisms that shape neural selectivity for visual forms in the human brain remain essentially unknown. Here, we combine behavioral and functional magnetic resonance imaging (fMRI) measurements to test the mechanisms that mediate enhanced behavioral sensitivity in the discrimination of visual forms after training. In particular, we used high-resolution fMRI and multivoxel pattern classification methods to investigate fine learning-dependent changes in neural preference for global forms. We measured the observers' choices when discriminating between concentric and radial patterns presented in noise before and after training. Similarly, we measured the choices of a pattern classifier when predicting each stimulus from fMRI activity. Comparing the performance of human observers and classifiers demonstrated that learning alters the observers' sensitivity to visual forms and the tuning of fMRI activation patterns in visual areas selective for task-relevant features. In particular, training on low-signal stimuli enhanced the amplitude but reduced the width of pattern-based tuning functions in higher dorsal and ventral visual areas. Thus, our findings suggest that learning of visual patterns is implemented by enhancing the response to the preferred stimulus category and reducing the response to nonpreferred stimuli in higher extrastriate visual cortex

Development of visual cortical function in infant macaques: A BOLD fMRI study.

Functional brain development is not well understood. In the visual system, neurophysiological studies in nonhuman primates show quite mature neuronal properties near birth although visual function is itself quite immature and continues to develop over many months or years after birth. Our goal was to assess the relative development of two main visual processing streams, dorsal and ventral, using BOLD fMRI in an attempt to understand the global mechanisms that support the maturation of visual behavior. Seven infant macaque monkeys (Macaca mulatta) were repeatedly scanned, while anesthetized, over an age range of 102 to 1431 days. Large rotating checkerboard stimuli induced BOLD activation in visual cortices at early ages. Additionally we used static and dynamic Glass pattern stimuli to probe BOLD responses in primary visual cortex and two extrastriate areas: V4 and MT-V5. The resulting activations were analyzed with standard GLM and multivoxel pattern analysis (MVPA) approaches. We analyzed three contrasts: Glass pattern present/absent, static/dynamic Glass pattern presentation, and structured/random Glass pattern form. For both GLM and MVPA approaches, robust coherent BOLD activation appeared relatively late in comparison to the maturation of known neuronal properties and the development of behavioral sensitivity to Glass patterns. Robust differential activity to Glass pattern present/absent and dynamic/static stimulus presentation appeared first in V1, followed by V4 and MT-V5 at older ages; there was no reliable distinction between the two extrastriate areas. A similar pattern of results was obtained with the two analysis methods, although MVPA analysis showed reliable differential responses emerging at later ages than GLM. Although BOLD responses to large visual stimuli are detectable, our results with more refined stimuli indicate that global BOLD activity changes as behavioral performance matures. This reflects an hierarchical development of the visual pathways. Since fMRI BOLD reflects neural activity on a population level, our results indicate that, although individual neurons might be adult-like, a longer maturation process takes place on a population level

The Extracellular Domain of Myelin Oligodendrocyte Glycoprotein Elicits Atypical Experimental Autoimmune Encephalomyelitis in Rat and Species

Atypical models of experimental autoimmune encephalomyelitis (EAE) are advantageous in that the heterogeneity of clinical signs appears more reflective of those in multiple sclerosis (MS). Conversely, models of classical EAE feature stereotypic progression of an ascending flaccid paralysis that is not a characteristic of MS. The study of atypical EAE however has been limited due to the relative lack of suitable models that feature reliable disease incidence and severity, excepting mice deficient in gamma-interferon signaling pathways. In this study, atypical EAE was induced in Lewis rats, and a related approach was effective for induction of an unusual neurologic syndrome in a cynomolgus macaque. Lewis rats were immunized with the rat immunoglobulin variable (IgV)-related extracellular domain of myelin oligodendrocyte glycoprotein (IgV-MOG) in complete Freund’s adjuvant (CFA) followed by one or more injections of rat IgV-MOG in incomplete Freund’s adjuvant (IFA). The resulting disease was marked by torticollis, unilateral rigid paralysis, forelimb weakness, and high titers of anti-MOG antibody against conformational epitopes of MOG, as well as other signs of atypical EAE. A similar strategy elicited a distinct atypical form of EAE in a cynomolgus macaque. By day 36 in the monkey, titers of IgG against conformational epitopes of extracellular MOG were evident, and on day 201, the macaque had an abrupt onset of an unusual form of EAE that included a pronounced arousal-dependent, transient myotonia. The disease persisted for 6–7 weeks and was marked by a gradual, consistent improvement and an eventual full recovery without recurrence. These data indicate that one or more boosters of IgV-MOG in IFA represent a key variable for induction of atypical or unusual forms of EAE in rat and Macaca species. These studies also reveal a close correlation between humoral immunity against conformational epitopes of MOG, extended confluent demyelinating plaques in spinal cord and brainstem, and atypical disease induction

Eggshell spot scoring methods cannot be used as a reliable proxy to determine pigment quantity

Article first published online: 4 DEC 2013Eggshell maculation of most passerines is due to the deposition of the pigment protoporphyrin which is produced during biosynthesis of blood haem. Its functional significance has only received empirical attention in recent years. This interest has generated a number of hypotheses of which some remain untested partly because the quantification of protoporphyrin is analytically challenging and can be prohibitively expensive. Many studies have therefore used the extent of eggshell spotting as a proxy for total eggshell protoporphyrin concentration, although this has not been formally tested. Pigment scoring involves recording visible eggshell pigment attributes, such as spot intensity, distribution and size. Since even immaculate eggs can contain some protoporphyrin, there remains doubt over the degree to which visible pigment correlates with total pigment content of the shell. In this study, we test whether visible pigment scoring can be used as a proxy for protoporphyrin concentration of an eggshell. We use pigmented eggshells of two common British passerine species to compare eggshell spot intensity, distribution and spot size (as used by the visual pigment scoring method) with direct measures of eggshell protoporphyrin concentration. In addition, we compared an alternative method of pigment scoring, the pixel pigment scoring method, using a computer programme to quantify the number of pixels exceeding a specified colour threshold. We demonstrate that although results from both scoring methods were positively correlated with eggshell protoporphyrin concentrations, the correlations were not sufficiently strong to be used as surrogates in studies where actual pigment concentrations are required.Kaat Brulez, Phillip Cassey, Alan Meeson, Ivan Mikšík, Simone L. Webber, Andrew G. Gosler and S. James Reynold

Data from: Development of visual cortical function in infant macaques: a BOLD fMRI study

Functional brain development is not well understood. In the visual system, neurophysiological studies in nonhuman primates show quite mature neuronal properties near birth although visual function is itself quite immature and continues to develop over many months or years after birth. Our goal was to assess the relative development of two main visual processing streams, dorsal and ventral, using BOLD fMRI in an attempt to understand the global mechanisms that support the maturation of visual behavior. Seven infant macaque monkeys (_Macaca mulatta_) were repeatedly scanned, while anesthetized, over an age range of 102 to 1431 days. Large rotating checkerboard stimuli induced BOLD activation in visual cortices at early ages. Additionally we used static and dynamic Glass pattern stimuli to probe BOLD responses in primary visual cortex and two extrastriate areas: V4 and MT-V5. The resulting activations were analyzed with standard GLM and multivoxel pattern analysis (MVPA) approaches. We analyzed three contrasts: Glass pattern present/absent, static/dynamic Glass pattern presentation, and structured/random Glass pattern form. For both GLM and MVPA approaches, robust coherent BOLD activation appeared relatively late in comparison to the maturation of known neuronal properties and the development of behavioral sensitivity to Glass patterns. Robust differential activity to Glass pattern present/absent and dynamic/static stimulus presentation appeared first in V1, followed by V4 and MT-V5 at older ages; there was no reliable distinction between the two extrastriate areas. A similar pattern of results was obtained with the two analysis methods, although MVPA analysis showed reliable differential responses emerging at later ages than GLM. Although BOLD responses to large visual stimuli are detectable, our results with more refined stimuli indicate that global BOLD activity changes as behavioral performance matures. This reflects an hierarchical development of the visual pathways. Since fMRI BOLD reflects neural activity on a population level, our results indicate that, although individual neurons might be adult-like, a longer maturation process takes place on a population level

Development of visual cortical function in infant macaques:A BOLD fMRI study

Functional brain development is not well understood. In the visual system, neurophysiological studies in nonhuman primates show quite mature neuronal properties near birth although visual function is itself quite immature and continues to develop over many months or years after birth. Our goal was to assess the relative development of two main visual processing streams, dorsal and ventral, using BOLD fMRI in an attempt to understand the global mechanisms that support the maturation of visual behavior. Seven infant macaque monkeys (Macaca mulatta) were repeatedly scanned, while anesthetized, over an age range of 102 to 1431 days. Large rotating checkerboard stimuli induced BOLD activation in visual cortices at early ages. Additionally we used static and dynamic Glass pattern stimuli to probe BOLD responses in primary visual cortex and two extrastriate areas: V4 and MT-V5. The resulting activations were analyzed with standard GLM and multivoxel pattern analysis (MVPA) approaches. We analyzed three contrasts: Glass pattern present/absent, static/dynamic Glass pattern presentation, and structured/random Glass pattern form. For both GLM and MVPA approaches, robust coherent BOLD activation appeared relatively late in comparison to the maturation of known neuronal properties and the development of behavioral sensitivity to Glass patterns. Robust differential activity to Glass pattern present/absent and dynamic/static stimulus presentation appeared first in V1, followed by V4 and MT-V5 at older ages; there was no reliable distinction between the two extrastriate areas. A similar pattern of results was obtained with the two analysis methods, although MVPA analysis showed reliable differential responses emerging at later ages than GLM. Although BOLD responses to large visual stimuli are detectable, our results with more refined stimuli indicate that global BOLD activity changes as behavioral performance matures. This reflects an hierarchical development of the visual pathways. Since fMRI BOLD reflects neural activity on a population level, our results indicate that, although individual neurons might be adult-like, a longer maturation process takes place on a population level

Infant fMRI data

Infant fMRI dat